Mercurial > repos > pjbriggs > pal_finder
changeset 12:d26fb5260c67 draft
0.02.04.6: update to use conda to resolve dependencies.
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--- a/README.rst Mon Jul 24 11:04:27 2017 -0400 +++ b/README.rst Thu Mar 15 09:49:05 2018 -0400 @@ -61,9 +61,10 @@ Version Changes ---------- ---------------------------------------------------------------------- -0.02.04.6 - Trap for errors in ``pal_finder_v0.02.04.pl`` resulting in bad - ranges being supplied to ``primer3_core`` for some reads via - ``PRIMER_PRODUCT_RANGE_SIZE``. +0.02.04.6 - Update to get dependencies using ``conda`` when installed from the + toolshed (this removes the explicit dependency on Perl 5.16 + introduced in 0.02.04.2, as a result the outputs from the tool are + now non-deterministic in some cases). 0.02.04.5 - Update to handle large output files which can sometimes be generated by the ``pal_finder_v0.02.04.pl`` or ``pal_filter.py`` scripts (logs of hundreds of Gb's have been observed in production): log files
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pal_finder_macros.xml Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,40 @@ +<macros> + <!-- + Set the path for the pal_finder data files + --> + <token name="@CONDA_PAL_FINDER_SCRIPT_DIR@">if [ -z "\$PALFINDER_SCRIPT_DIR" ]; then export PALFINDER_SCRIPT_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi</token> + <token name="@CONDA_PAL_FINDER_DATA_DIR@">if [ -z "\$PALFINDER_DATA_DIR" ]; then export PALFINDER_DATA_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi</token> + <xml name="output_illumina_microsat_summary"> + <output name="output_microsat_summary"> + <assert_contents> + <has_line line="allExtended:	0" /> + <has_line line="allSpan:	0" /> + <has_line line="broken:	2" /> + <has_line line="compound:	2" /> + <has_line line="readsWithMicrosat:	13" /> + <has_line line="totalBases:	2320" /> + <has_line line="totalReads:	20	(2 x 10)" /> + <has_line line="Microsat Type	monomer length	total loci	loci w/ primers	reads with loci	total bases	extended	extended w/ primers	spanning	spanning w/ primers" /> + <has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" /> + <has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" /> + <has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" /> + </assert_contents> + </output> + </xml> + <xml name="output_454_microsat_summary"> + <output name="output_microsat_summary"> + <assert_contents> + <has_line line="broken:	1" /> + <has_line line="compound:	0" /> + <has_line line="readsWithMicrosat:	1" /> + <has_line line="readsWithPrimers:	0" /> + <has_line line="totalBases:	8639" /> + <has_line line="totalReads:	38" /> + <has_line line="Microsat Type	monomer length	reads with loci	total loci	loci amplified	total loci bases	loci bases amplified" /> + <has_line_matching expression="(AC|TG)\t2\t.*" /> + <has_line_matching expression="(AT|CG)\t2\t0\t0\t0\t0\t0" /> + <has_line_matching expression="(AG|TC)\t2\t0\t0\t0\t0\t0" /> + </assert_contents> + </output> + </xml> +</macros>
--- a/pal_finder_wrapper.sh Mon Jul 24 11:04:27 2017 -0400 +++ b/pal_finder_wrapper.sh Thu Mar 15 09:49:05 2018 -0400 @@ -53,9 +53,6 @@ # Maximum size reporting log file contents MAX_LINES=500 # -# Get helper functions -. $(dirname $0)/pal_finder_wrapper_utils.sh -# # Initialise locations of scripts, data and executables # # Set these in the environment to overide at execution time @@ -66,18 +63,31 @@ # Filter script is in the same directory as this script PALFINDER_FILTER=$(dirname $0)/pal_filter.py if [ ! -f $PALFINDER_FILTER ] ; then - fatal No $PALFINDER_FILTER script + echo No $PALFINDER_FILTER script >&2 + exit 1 fi # # Check that we have all the components +function have_program() { + local program=$1 + local got_program=$(which $program 2>&1 | grep "no $(basename $program) in") + if [ -z "$got_program" ] ; then + echo yes + else + echo no + fi +} if [ "$(have_program $PRIMER3_CORE_EXE)" == "no" ] ; then - fatal "primer3_core missing: ${PRIMER3_CORE_EXE} not found" + echo "ERROR primer3_core missing: ${PRIMER3_CORE_EXE} not found" >&2 + exit 1 fi if [ ! -f "${PALFINDER_DATA_DIR}/config.txt" ] ; then - fatal "pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" + echo "ERROR pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" >&2 + exit 1 fi if [ ! -f "${PALFINDER_SCRIPT_DIR}/pal_finder_v0.02.04.pl" ] ; then - fatal "pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" + echo "ERROR pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" >&2 + exit 1 fi # # Initialise parameters used in the config.txt file @@ -108,7 +118,7 @@ if [ $# -lt 2 ] ; then echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" - fatal "Bad command line" + exits fi if [ "$1" == "--454" ] ; then PLATFORM="454" @@ -225,14 +235,16 @@ # Check that primer3_core is available got_primer3=`which $PRIMER3_CORE_EXE 2>&1 | grep -v "no primer3_core in"` if [ -z "$got_primer3" ] ; then - fatal "primer3_core not found" + echo ERROR primer3_core not found >&2 + exit 1 fi # # Set up the working dir if [ "$PLATFORM" == "Illumina" ] ; then # Paired end Illumina data as input if [ $FASTQ_R1 == $FASTQ_R2 ] ; then - fatal ERROR R1 and R2 fastqs are the same file + echo ERROR R1 and R2 fastqs are the same file >&2 + exit 1 fi ln -s $FASTQ_R1 ln -s $FASTQ_R2 @@ -252,6 +264,17 @@ /bin/cp $PALFINDER_DATA_DIR/config.txt . # # Update the config.txt file with new values +function set_config_value() { + local key=$1 + local value=$2 + local config_txt=$3 + if [ -z "$value" ] ; then + echo "No value for $key, left as default" + else + echo Setting "$key" to "$value" + sed -i 's,^'"$key"' .*,'"$key"' '"$value"',' $config_txt + fi +} # Input files set_config_value platform $PLATFORM config.txt if [ "$PLATFORM" == "Illumina" ] ; then @@ -276,7 +299,6 @@ # Primer3 settings set_config_value primer3input Output/pr3in.txt config.txt set_config_value primer3output Output/pr3out.txt config.txt -set_config_value keepPrimer3files 1 config.txt set_config_value primer3executable $PRIMER3_CORE_EXE config.txt set_config_value prNamePrefix ${PRIMER_PREFIX}_ config.txt set_config_value PRIMER_MISPRIMING_LIBRARY "$PRIMER_MISPRIMING_LIBRARY" config.txt @@ -307,32 +329,20 @@ # # Check that log ends with "Done!!" message if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then - fatal ERROR pal_finder failed to complete successfully -fi -echo "### pal_finder finished ###" -# -# Check for errors in pal_finder output -echo "### Checking for errors ###" -if [ ! -z "$(grep 'primer3_core: Illegal element in PRIMER_PRODUCT_SIZE_RANGE' pal_finder.log)" ] ; then - echo ERROR primer3 terminated prematurely due to bad product size ranges - cat >&2 <<EOF -ERROR primer3 terminated prematurely due to bad product size ranges - -Pal_finder generated bad ranges for the following read IDs: -EOF - echo $(find_bad_primer_ranges Output/pr3in.txt) >&2 - cat >&2 <<EOF - -This error can occur when input data contains short R1 reads and has -has not been properly trimmed and filtered. - -EOF - fatal pal_finder failed to complete successfully -EOF + echo ERROR pal_finder failed to complete successfully >&2 + exit 1 fi # -# Sort outputs into a consistent order regardless of Perl version -echo "### Sorting outputs ###" +# Sort microsat_summary output +echo "### Sorting microsat summary output ###" +head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted +grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted +grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted +tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted +mv microsat_summary.sorted Output/microsat_summary.txt +# +# Sort PAL_summary output +echo "### Sorting PAL summary output ###" head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt if [ "$PLATFORM" == "Illumina" ] ; then grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt @@ -352,9 +362,11 @@ fi tail -$MAX_LINES pal_filter.log if [ $? -ne 0 ] ; then - fatal $PALFINDER_FILTER exited with non-zero status + echo ERROR $PALFINDER_FILTER exited with non-zero status >&2 + exit 1 elif [ ! -f PAL_summary.filtered ] ; then - fatal no output from $PALFINDER_FILTER + echo ERROR no output from $PALFINDER_FILTER >&2 + exit 1 fi fi # @@ -374,7 +386,8 @@ if [ -f "$assembly" ] ; then /bin/mv $assembly "$OUTPUT_ASSEMBLY" else - fatal no assembly output found + echo ERROR no assembly output found >&2 + exit 1 fi fi if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then
--- a/pal_finder_wrapper.xml Mon Jul 24 11:04:27 2017 -0400 +++ b/pal_finder_wrapper.xml Thu Mar 15 09:49:05 2018 -0400 @@ -1,13 +1,18 @@ <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6"> <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description> + <macros> + <import>pal_finder_macros.xml</import> + </macros> <requirements> - <requirement type="package" version="5.16.3">perl</requirement> <requirement type="package" version="0.02.04">pal_finder</requirement> - <requirement type="package" version="2.0.0">primer3_core</requirement> + <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">biopython</requirement> <requirement type="package" version="2.8.1">pandaseq</requirement> </requirements> - <command interpreter="bash">pal_finder_wrapper.sh + <command><![CDATA[ + @CONDA_PAL_FINDER_SCRIPT_DIR@ && + @CONDA_PAL_FINDER_DATA_DIR@ && + bash $__tool_directory__/pal_finder_wrapper.sh #if str( $platform.platform_type ) == "illumina" #set $paired_input_type = $platform.paired_input_type_conditional.paired_input_type #if $paired_input_type == "pair_of_files" @@ -57,7 +62,7 @@ $platform.assembly "$output_assembly" #end if #end if - </command> + ]]></command> <inputs> <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" /> <conditional name="platform"> @@ -169,18 +174,18 @@ </data> </outputs> <tests> + <!-- Test with Illumina input --> <test> - <!-- Test with Illumina input --> <param name="platform_type" value="illumina" /> <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> - <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> - <output name="output_pal_summary" file="illuminaPE_microsats.out" /> - <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" /> + <expand macro="output_illumina_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> + <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" /> <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" /> </test> + <!-- Test with Illumina input as dataset pair --> <test> - <!-- Test with Illumina input as dataset pair --> <param name="platform_type" value="illumina" /> <param name="paired_input_type" value="collection" /> <param name="input_fastq_pair"> @@ -189,64 +194,65 @@ <element name="reverse" value="illuminaPE_r2.fq" ftype="fastqsanger" /> </collection> </param> - <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> - <output name="output_pal_summary" file="illuminaPE_microsats.out" /> - <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" /> + <expand macro="output_illumina_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> + <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" /> <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" /> </test> + <!-- Test with Illumina input filter to loci with PandaSEQ assembly + ('-assembly' option) + --> <test> - <!-- Test with Illumina input filter to loci with PandaSEQ assembly - ('-assembly' option) --> <param name="platform_type" value="illumina" /> <param name="filters" value="" /> <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> - <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> - <output name="output_pal_summary" file="illuminaPE_microsats.out" /> + <expand macro="output_illumina_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> <output name="output_assembly" file="illuminaPE_assembly.out" /> </test> + <!-- Test with Illumina input filter to loci with primers + ('-primers' option) --> <test> - <!-- Test with Illumina input filter to loci with primers - ('-primers' option) --> <param name="platform_type" value="illumina" /> <param name="filters" value="-primers" /> <param name="assembly" value="false" /> <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> - <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> - <output name="output_pal_summary" file="illuminaPE_microsats.out" /> - <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_primers.out" /> + <expand macro="output_illumina_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> + <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_primers.out.re_match" /> </test> + <!-- Test with Illumina input filter to loci which appear only once + ('-occurrences' option) --> <test> - <!-- Test with Illumina input filter to loci which appear only once - ('-occurrences' option) --> <param name="platform_type" value="illumina" /> <param name="filters" value="-occurrences" /> <param name="assembly" value="false" /> <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> - <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> - <output name="output_pal_summary" file="illuminaPE_microsats.out" /> - <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_occurrences.out" /> + <expand macro="output_illumina_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> + <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_occurrences.out.re_match" /> </test> + <!-- Test with Illumina input filter and rank loci with perfect motifs + ('-rankmotifs' option) --> <test> - <!-- Test with Illumina input filter and rank loci with perfect motifs - ('-rankmotifs' option) --> <param name="platform_type" value="illumina" /> <param name="filters" value="-rankmotifs" /> <param name="assembly" value="false" /> <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> - <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> - <output name="output_pal_summary" file="illuminaPE_microsats.out" /> - <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_rankmotifs.out" /> + <expand macro="output_illumina_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> + <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" /> </test> + <!-- Test with 454 input --> <test> - <!-- Test with 454 input --> <param name="platform_type" value="454" /> <param name="input_fasta" value="454_in.fa" ftype="fasta" /> - <output name="output_microsat_summary" file="454_microsat_types.out" /> - <output name="output_pal_summary" file="454_microsats.out" /> + <expand macro="output_454_microsat_summary" /> + <output name="output_pal_summary" compare="re_match" file="454_microsats.out.re_match" /> </test> </tests> <help> @@ -274,29 +280,6 @@ ------------- -.. class:: warning - -**Known problems** - -.. class:: infomark - -**Bad primer product size ranges** - -For some datasets pal_finder may generate 'bad' product size ranges (where the -lower limit exceeds the upper limit) for one or more reads, for input into -primer3_core. - -If this occurs then the tool will terminate with an error. A list of the reads -for which the bad ranges were generated can be found in the error message -which can be accessed via the 'bug' icon from a failed dataset. - -The conditions which cause this error are unclear. However we believe it to be -associated with short or low quality reads. It is recommended that the input -data are sufficiently trimmed and filtered (using e.g. the Trimmomatic tool) -before rerunning pal_finder. - -------------- - .. class:: infomark **Credits**
--- a/pal_finder_wrapper_utils.sh Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -#!/bin/bash -# -# Helper functions for the pal_finder_wrapper.sh script -# -# Utility function for terminating on fatal error -function fatal() { - echo "FATAL $@" >&2 - exit 1 -} -# -# Check that specified program is available -function have_program() { - local program=$1 - local got_program=$(which $program 2>&1 | grep "no $(basename $program) in") - if [ -z "$got_program" ] ; then - echo yes - else - echo no - fi -} -# -# Set the value for a parameter in the pal_finder config file -function set_config_value() { - local key=$1 - local value=$2 - local config_txt=$3 - if [ -z "$value" ] ; then - echo "No value for $key, left as default" - else - echo Setting "$key" to "$value" - sed -i 's,^'"$key"' .*,'"$key"' '"$value"',' $config_txt - fi -} -# -# Identify 'bad' PRIMER_PRODUCT_SIZE_RANGE from pr3in.txt file -function find_bad_primer_ranges() { - # Parses a pr3in.txt file from pal_finder and reports - # sequence ids where the PRIMER_PRODUCT_SIZE_RANGE has - # upper limit which is smaller than lower limit - local pr3in=$1 - local pattern="^(SEQUENCE_ID|PRIMER_PRODUCT_SIZE_RANGE)" - for line in $(grep -E "$pattern" $pr3in | sed 's/ /^/' | sed 'N;s/\n/*/') - do - # Loop over pairs of SEQUENCE_ID and PRIMER_PRODUCT_SIZE_RANGE - # keywords in the primer3 input - if [ ! -z "$(echo $line | grep ^SEQUENCE_ID)" ] ; then - # Extract the values - local size_range=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2 | tr '^' ' ') - local seq_id=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2) - else - local size_range=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2) - local seq_id=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2) - fi - seq_id=$(echo $seq_id | cut -d')' -f3) - # Check the upper and lower limits in each range - # to see if it's okay - local bad_range= - for range in $(echo $size_range) ; do - local lower=$(echo $range | cut -d'-' -f1) - local upper=$(echo $range | cut -d'-' -f2) - if [ $lower -gt $upper ] ; then - bad_range=yes - break - fi - done - # Report if the range is wrong - if [ ! -z "$bad_range" ] ; then - echo "$seq_id ($size_range)" - fi - done -}
--- a/test-data/454_microsat_types.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -totalBases: 8639 -readsWithPrimers: 0 -totalReads: 38 -compound: 0 -broken: 1 -readsWithMicrosat: 1 - - -Microsat Type monomer length reads with loci total loci loci amplified total loci bases loci bases amplified -TC 2 0 0 0 0 0 -AC 2 1 2 0 48 0 -CG 2 0 0 0 0 0 -AT 2 0 0 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/454_microsat_types.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,14 @@ + +broken\:\ 1 +compound\:\ 0 +readsWithMicrosat\:\ 1 +readsWithPrimers\:\ 0 +totalBases\:\ 8639 +totalReads\:\ 38 + + +Microsat\ Type\ monomer\ length\ reads\ with\ loci\ total\ loci\ loci\ amplified\ total\ loci\ bases\ loci\ bases\ amplified +AC\ 2\ 1\ 2\ \ 48\ +AT\ 2\ 0\ 0\ 0\ 0\ 0 +CG\ 2\ 0\ 0\ 0\ 0\ 0 +TG\ 2\ 0\ 0\ 0\ 0\ 0
--- a/test-data/454_microsats.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -SequenceID Repeat Motif Size Repeat Motif Number Tandem Repeats Primer Designed (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Total Repeats In Amplicon Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs -FW1N29Q04EP35X 2 AC 18 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/454_microsats.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,2 @@ +SequenceID\ Repeat\ Motif\ Size\ Repeat\ Motif\ Number\ Tandem\ Repeats\ Primer\ Designed\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Total\ Repeats\ In\ Amplicon\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +FW1N29Q04EP35X\ 2\ (AC|TG)\ 18\ 0\ \ \ \ \ \ \ \ \
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/454_microsats.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,2 @@ +SequenceID\ Repeat\ Motif\ Size\ Repeat\ Motif\ Number\ Tandem\ Repeats\ Primer\ Designed\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Total\ Repeats\ In\ Amplicon\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +FW1N29Q04EP35X\ 2\ AC\ 18\ 0\ \ \ \ \ \ \ \ \
--- a/test-data/illuminaPE_filtered_microsats.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)\(14\)\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC\(12\)\ \ 12\ \ \ 1\ test\_3\ AAGTACAGTGGGGAGGCTGG\ test\_6\ TTTTCTACACAGCTCAAGTAGCCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC\(12\)\ \ 12\ \ \ 1\ test\_7\ GCAGTAAACAAAGGCAAAGGG\ test\_4\ CCTGGGCAGAGGTGTTCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ AG\(14\)\ \ 14\ \ \ 1\ test\_5\ TTCTCCCACTATATTTTGCATTGG\ test\_1\ TCCAGACTGAAGCTACCCTGG\ AG\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- a/test-data/illuminaPE_filtered_microsats_occurrences.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)\(14\)\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ AG\(14\)\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_6\ TCCAGACTGAAGCTACCCTGG\ AG\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC\(12\)\ \ 12\ \ \ 1\ test\_5\ GCAGTAAACAAAGGCAAAGGG\ test\_2\ CCTGGGCAGAGGTGTTCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC\(12\)\ \ 12\ \ \ 1\ test\_8\ AAGTACAGTGGGGAGGCTGG\ test\_4\ TTTTCTACACAGCTCAAGTAGCCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC
--- a/test-data/illuminaPE_filtered_microsats_primers.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC -ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 AC(12) AC(12) 24 1 test_2 TCTTTATCTAAACACATCCTGAAATACC test_1 AAACGCAATTATTTTGAGATGTCC AC(12) AC(12) 24 1 1 2 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 1:N:0:TCCTGA TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC >ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 2:N:0:TCCTGA TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_primers.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,5 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)\(14\)\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ (AC|TG)\(12\)\ (AC|TG)\(12\)\ \ 24\ \ \ 1\ test\_.*\ TCTTTATCTAAACACATCCTGAAATACC\ test\_.*\ AAACGCAATTATTTTGAGATGTCC\ (AC|TG)\(12\)\ (AC|TG)\(12\)\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\ TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\ TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_primers.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,5 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ AG\(14\)\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_2\ TCCAGACTGAAGCTACCCTGG\ AG\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ TG\(12\)\ \ 12\ \ \ 1\ test\_5\ GCAGTAAACAAAGGCAAAGGG\ test\_3\ CCTGGGCAGAGGTGTTCC\ TG\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ TG\(12\)\ \ 12\ \ \ 1\ test\_4\ AAGTACAGTGGGGAGGCTGG\ test\_6\ TTTTCTACACAGCTCAAGTAGCCC\ TG\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ TG\(12\)\ TG\(12\)\ \ 24\ \ \ 1\ test\_8\ TCTTTATCTAAACACATCCTGAAATACC\ test\_1\ AAACGCAATTATTTTGAGATGTCC\ TG\(12\)\ TG\(12\)\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\ TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\ TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC
--- a/test-data/illuminaPE_filtered_microsats_rankmotifs.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC -ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 AT(12) 12 0 >ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 1:N:0:TCCTGA TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG >ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 2:N:0:TCCTGA TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT -ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 TC(12) 12 0 >ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 1:N:0:TCCTGA TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA >ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 2:N:0:TCCTGA TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA -ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 AT(12) 12 0 >ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 1:N:0:TCCTGA TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC >ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 2:N:0:TCCTGA TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 AC(36) 36 0 >ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 1:N:0:TCCTGA TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA >ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 2:N:0:TCCTGA TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,8 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\ TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\ TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ (AG|TC)\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ (AC|TG)\(36\)\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\ TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\ TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)\(14\)\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,8 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC\(12\)\ \ 12\ \ \ 1\ test\_3\ AAGTACAGTGGGGAGGCTGG\ test\_4\ TTTTCTACACAGCTCAAGTAGCCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\ TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\ TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ TC\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC\(12\)\ \ 12\ \ \ 1\ test\_6\ GCAGTAAACAAAGGCAAAGGG\ test\_1\ CCTGGGCAGAGGTGTTCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ AC\(36\)\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\ TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\ TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ TC\(14\)\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_2\ TCCAGACTGAAGCTACCCTGG\ TC\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA
--- a/test-data/illuminaPE_microsat_types.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -totalBases: 2320 -allSpan: 0 -totalReads: 20 (2 x 10) -compound: 2 -broken: 2 -allExtended: 0 -readsWithMicrosat: 13 - - -Microsat Type monomer length total loci loci w/ primers reads with loci total bases extended extended w/ primers spanning spanning w/ primers -TC 2 2 1 2 26 0 0 0 0 -AC 2 7 4 7 116 0 0 0 0 -CG 2 0 0 0 0 0 0 0 0 -AT 2 8 0 6 106 0 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsat_types.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,16 @@ +allExtended\:\ 0 +allSpan\:\ 0 +broken\:\ 2 +compound\:\ 2 +readsWithMicrosat\:\ 13 +totalBases\:\ 2320 +totalReads\:\ 20\ \(2\ x\ 10\) + + +Microsat\ Type\ monomer\ length\ total\ loci\ loci\ w\/\ primers\ reads\ with\ loci\ total\ bases\ extended\ extended\ w\/\ primers\ spanning\ spanning\ w\/\ primers +(AC\ 2\ 7\ 4\ 7\ 116\ 0\ 0\ 0\ 0)? +(AG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0)? +(AT\ 2\ 8\ 0\ 6\ 106\ 0\ 0\ 0\ 0)? +CG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0 +TC\ 2\ 2\ 1\ 2\ 26\ \ \ \ +(TG\ 2\ 7\ 4\ 7\ 116\ \ \ \ )? \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsat_types.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,15 @@ +allExtended\:\ 0 +allSpan\:\ 0 +broken\:\ 2 +compound\:\ 2 +readsWithMicrosat\:\ 13 +totalBases\:\ 2320 +totalReads\:\ 20\ \(2\ x\ 10\) + + +Microsat\ Type\ monomer\ length\ total\ loci\ loci\ w\/\ primers\ reads\ with\ loci\ total\ bases\ extended\ extended\ w\/\ primers\ spanning\ spanning\ w\/\ primers +AC\ 2\ 7\ 4\ 7\ 116\ 0\ 0\ 0\ 0 +AG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0 +AT\ 2\ 8\ 0\ 6\ 106\ 0\ 0\ 0\ 0 +CG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0 +TC\ 2\ 2\ 1\ 2\ 26\ \ \ \
--- a/test-data/illuminaPE_microsats.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 -ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 AC(36) 36 0 -ILLUMINA-545855:49:FC61RLR:2:1:19063:1614 AT(14) AT(14) AT(14) AT(14) 56 0 -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 -ILLUMINA-545855:49:FC61RLR:2:1:5626:1554 AT(14) AC(16) AC(16) AT(12) 58 0 -ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 AT(12) 12 0 -ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 TC(12) 12 0 -ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 AT(12) 12 0 -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 -ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 AC(12) AC(12) 24 1 test_2 TCTTTATCTAAACACATCCTGAAATACC test_1 AAACGCAATTATTTTGAGATGTCC AC(12) AC(12) 24 1 1 2 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsats.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,11 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)\(14\)\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ (AC|TG)\(36\)\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\ AT\(14\)\ AT\(14\)\ AT\(14\)\ AT\(14\)\ \ 56\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\ AT\(14\)\ (AC|TG)\(16\)\ (AC|TG)\(16\)\ AT\(12\)\ \ 58\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ (AG|TC)\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)\(12\)\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ (AC|TG)\(12\)\ (AC|TG)\(12\)\ \ 24\ \ \ 1\ test\_.*\ TCTTTATCTAAACACATCCTGAAATACC\ test\_.*\ AAACGCAATTATTTTGAGATGTCC\ (AC|TG)\(12\)\ (AC|TG)\(12\)\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsats.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,11 @@ +readPairID\ Motifs\(bases\)\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ \(1\=y\,0\=n\)\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ TC\(14\)\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_2\ TCCAGACTGAAGCTACCCTGG\ TC\(14\)\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ AC\(36\)\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\ AT\(14\)\ AT\(14\)\ AT\(14\)\ AT\(14\)\ \ 56\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC\(12\)\ \ 12\ \ \ 1\ test\_6\ GCAGTAAACAAAGGCAAAGGG\ test\_1\ CCTGGGCAGAGGTGTTCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\ AT\(14\)\ AC\(16\)\ AC\(16\)\ AT\(12\)\ \ 58\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ TC\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT\(12\)\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC\(12\)\ \ 12\ \ \ 1\ test\_3\ AAGTACAGTGGGGAGGCTGG\ test\_4\ TTTTCTACACAGCTCAAGTAGCCC\ AC\(12\)\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ AC\(12\)\ AC\(12\)\ \ 24\ \ \ 1\ test\_8\ TCTTTATCTAAACACATCCTGAAATACC\ test\_5\ AAACGCAATTATTTTGAGATGTCC\ AC\(12\)\ AC\(12\)\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1
--- a/tool_dependencies.xml Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="pal_finder" version="0.02.04"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz</action> - <action type="move_file"> - <source>pal_finder_v0.02.04.pl</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>config.txt</source> - <destination>$INSTALL_DIR/data</destination> - </action> - <action type="move_file"> - <source>simple.ref</source> - <destination>$INSTALL_DIR/data</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="PALFINDER_SCRIPT_DIR" action="set_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="PALFINDER_DATA_DIR" action="set_to">$INSTALL_DIR/data</environment_variable> - </action> - </actions> - </install> - <readme>pal_finder also needs Perl</readme> - </package> - <package name="perl" version="5.16.3"> - <install version="1.0"> - <actions> - <!-- install perl --> - <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.16.3.tar.gz</action> - <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action> - <action type="make_install" /> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Perl 5 is a highly capable, feature-rich programming language with over 25 years of - development: - - http://www.perl.org/ - </readme> - </package> - <package name="primer3_core" version="2.0.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://sourceforge.net/projects/primer3/files/primer3/2.0.0-alpha/primer3-2.0.0-alpha.tar.gz</action> - <action type="shell_command">make -C src -f Makefile</action> - <action type="move_file"> - <source>src/primer3_core</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>primer3_core</readme> - </package> - <package name="biopython" version="1.65"> - <install version="1.0"> - <actions> - <action type="shell_command">pip install --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action> - <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable> - <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib64/python2.7/site-packages</environment_variable> - </action> - </actions> - </install> - <readme>BioPython 1.65</readme> - </package> - <package name="pandaseq" version="2.8.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz</action> - <action type="shell_command">./autogen.sh</action> - <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> - <action type="shell_command">make</action> - <action type="shell_command">make install</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> - </action> - </actions> - </install> - <readme>PANDASeq 2.8.1 - - PANDASEQ is a program to align Illumina reads, optionally - with PCR primers embedded in the sequence, and reconstruct - an overlapping sequence. - - https://github.com/neufeld/pandaseq - </readme> - </package> -</tool_dependency>